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- PDB-7nml: Galectin-1 in complex with 4-Amino-6-chloro-1,3-benzenedisulfonamide -

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Basic information

Entry
Database: PDB / ID: 7nml
TitleGalectin-1 in complex with 4-Amino-6-chloro-1,3-benzenedisulfonamide
ComponentsGalectin-1
KeywordsCARBOHYDRATE / Galectin-1
Function / homology
Function and homology information


galectin complex / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / carbohydrate binding ...galectin complex / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / carbohydrate binding / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / positive regulation of viral entry into host cell / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / extracellular space / RNA binding / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
4-AMINO-6-CHLOROBENZENE-1,3-DISULFONAMIDE / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsGrimm, C. / Bechold, J. / Seibel, J.
CitationJournal: To Be Published
Title: Galectin-1 in complex with 4-Amino-6-chloro-1,3-benzenedisulfonamide
Authors: Grimm, C. / Bechold, J. / Seibel, J.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2689
Polymers29,5142
Non-polymers7557
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint14 kcal/mol
Surface area12340 Å2
Unit cell
Length a, b, c (Å)43.319, 58.475, 112.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Galectin-1 / / Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L- ...Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / HBL / HPL / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / Putative MAPK-activating protein PM12 / S-Lac lectin 1


Mass: 14756.753 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-I7B / 4-AMINO-6-CHLOROBENZENE-1,3-DISULFONAMIDE


Mass: 285.728 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8ClN3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.43→40.4 Å / Num. obs: 52116 / % possible obs: 97 % / Redundancy: 6.56 % / Biso Wilson estimate: 17.61 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.17
Reflection shellResolution: 1.43→1.481 Å / Num. unique obs: 32857 / CC1/2: 0.466

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4q26

4q26


Resolution: 1.43→40.4 Å / SU ML: 0.1871 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.6198
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 2100 4.03 %
Rwork0.1761 49983 -
obs0.1775 52083 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.59 Å2
Refinement stepCycle: LAST / Resolution: 1.43→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 40 242 2341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01152247
X-RAY DIFFRACTIONf_angle_d1.09983052
X-RAY DIFFRACTIONf_chiral_restr0.1081325
X-RAY DIFFRACTIONf_plane_restr0.0063409
X-RAY DIFFRACTIONf_dihedral_angle_d19.4171822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.460.39721310.38233135X-RAY DIFFRACTION93.42
1.46-1.50.35311370.33363255X-RAY DIFFRACTION96.17
1.5-1.540.37431370.30023261X-RAY DIFFRACTION96.53
1.54-1.590.2951360.26883236X-RAY DIFFRACTION96.37
1.59-1.640.31311370.25243246X-RAY DIFFRACTION96.74
1.64-1.70.28961380.223288X-RAY DIFFRACTION97.08
1.7-1.760.24031380.18523286X-RAY DIFFRACTION97.05
1.76-1.840.22451390.1623326X-RAY DIFFRACTION97.77
1.84-1.940.20061400.13943317X-RAY DIFFRACTION97.71
1.94-2.060.17441410.13313373X-RAY DIFFRACTION98.46
2.06-2.220.16291420.12993363X-RAY DIFFRACTION98.4
2.22-2.440.21581410.14993372X-RAY DIFFRACTION98.38
2.45-2.80.21361440.16673423X-RAY DIFFRACTION99.08
2.8-3.530.16871450.16463462X-RAY DIFFRACTION99.28
3.53-40.40.20051540.17443640X-RAY DIFFRACTION99.29

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